title: mRNA profiling of Trihelix transcription factor ASIL mutants in seedlings

summary: The current study aimed at exploring the roles of ASIL1 and ASIL2 trihelix transcription factors in repressing the maturation program during seedling development

overall_design: mRNA profiling was performed on 14 day seedlings in single (asil1-1, asil2-1, asil2-2) and double ASIL mutants (asil1-1 asil2-1, asil1-1 asil2-2), as well as their corresponding wild-type ecotype (Columbia-0 for asil1-1 and asil2-1; Landsberg erecta for asil2-2).  Three biological replicates were collected for each genotype.


title: Genomic and transcriptomic analyses of valencia orange provide insights into its domestication and traits formation

status: Public on Aug 26 2021

city: Wuhan

first: Guizhi

last: FENG

state: Hubei

address: No.1 of Shizishan street, Hongshan District

country: China

institute: Huazhong Agricultral University

type: Expression profiling by high throughput sequencing

summary: Valencia orange (Citrus sinensis Osbeck), namely summer orange (SO), is a type of late-ripening sweet oranges, the ripening time of which is 4 to 5 months later than that of the middle-ripening common sweet orange (CO). The mastication of SO fruit pulp is worse than that of CO. To date, how the late-ripening and poor pulp mastication traits were domesticated in SO is unknown. In this study, 13 SO cultivars and 12 CO cultivars were used for whole-genome resequencing. Population genetic diversity analysis divided these 25 samples into SO and CO subgroups, respectively. There were 144 and 141 genes identified by selective sweep analysis to be strongly selected during SO and CO evolutionary processes, respectively. Based on gene functional annotation and pathway enrichment analysis, most of these selected genes in SO were related to resistance and lignin biosynthesis. Simultaneously, we comparatively analyzed the transcriptome profiles of the peel and pulp tissues among three SO cultivars and three CO cultivars, which also revealed the difference of lignin synthesis between SO and CO fruits. Moreover, according to the comparative analysis of the lignin content and the expressions of the genes related to lignin biosynthesis in SO and CO fruits, we suggested that lignin may play an important role in the pulp mastication trait of SO. In addition, a SNP molecular marker was developed to distinguish SO and CO. This study reveals that the mastication trait may be formed in the process of SO domestication, while the late-ripening trait may be formed in a genetic mutation event.

overall_design: We performed a comparative fruit transcriptome analysis on three SO cultivars and three CO cultivars.

last: Feng

first: Juxun

last: Wu


title: Otulin inhibits RIPK1-mediated keratinocyte necroptosis to prevent skin inflammation in mice

status: Public on Aug 23 2021

city: Cologne

first: Manolis

last: Pasparakis

address: Joseph-Stelzmann-Str. 26

country: Germany

institute: University of Cologne

summary: Mice with epidermal keratinocyte specific knockout of OTULIN develop inflammatory skin disease. To study the inflammatory response we used Lexogen 3´mRNA sequencing to compare the gene expression profiles in the skin of OTULIN epidermis specific knockout and control mice.

overall_design: Skin samples were collected from 3-week old mice (OTULIN-KO, WT) for RNA extraction and subsequent 3´mRNA Sequencing.

first: Hannah

last: Schünke

first: Ulrike

last: Göbel


title: Characterization of pancreatic progenitor differentiation with GiBi-generated DE cells

city: University park

first: Yuqian

last: Jiang

state: PA

address: W345 millennium science complex

country: USA

institute: PSU

summary: We report the GiBi protocol to generate functional DE cells that can further enter pancreatic lineages. To understand the transcriptome dynamics during the generation of these pancreatic progenitor cells, we harvested cells at different time points of the differentiation for RNA sequencing. We find that during this process, genes that are related to pluripotency maintenance were decreasing and gastrulation-related genes were transiently expressed  in the middle. More importantly, genes that are critical in pancreatic specification got significantly upregulated across the differentiation.

overall_design: Every other day from D0 to D14 of the pancreatic progenitor differentiation, two biological replicates for each time point, we harvested in total 14 samples for RNA sequencing.

first: Xiaojun

last: Lian


title: PLD3 and PLD4 limit autoinflammation through multiple sensors of RNA and DNA.

status: Public on Aug 25 2021

city: La Jolla

first: Padma

last: Natarajan

state: CA

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

summary: Supplementary Figure 14. RNAseq analysis of Pld3–/–Pld4–/– liver.  Poly A+ RNA from whole livers were compared using next generation sequencing and the genes showing significant differences in expression from control livers of age-matched mice were further analyzed.

overall_design: RNA-Seq analyses were performed to identify differentially expressed genes in two datasets (Experiment1 and Experiment2 respectively) with 12 samples in each. Each dataset has 4 conditions with n=3 mice per condition.   Experiment 1. Comparison of liver RNAs from 2 week old C57BL/6, Pld3–/–, Pld4–/–, and Pld3–/–Pld4–/– mice.   Experiment 2. Comparison of liver RNAs from 2 month old C57BL/6, Tlr9CpG11/CpG11, Tlr9CpG11/CpG11Pld3–/–Pld4–/– and Unc93b13d/3dPld3–/–Pld4–/– mice.

first: David

last: Nemazee

first: Amanda

last: Gavin


title: Landscape of Star-PAP mRNA association along with its co-regulator RBM10 using HITS-CLIP (high-throughput sequencing coupled with cross-linking immunoprecipitation).

city: Trivandrum

first: Rakesh

middle: S

last: Laishram

state: Kerala

address: Thycaud P O, Poojappura

department: Cardiovascular and Diabetes Biology Group

country: India

institute: Rajiv Gandhi Centre for Biotechnology(RGCB)

summary: We employed HITS-CLIP to map genome wide Star-PAP mRNA binding and define the role of RBM10 on global Star-PAP mRNA association. We show a transcriptome-wide association of Star-PAP which is diminished on cellular Star-PAP depletion. HITs-CLIP data analysis of RBM10 knockdown and pulldown with anti Star-PAP antibody on HEK293 cells indicates significance of RBM10 in Star-PAP and mRNA association.

overall_design: Star-PAP HITS-CLIP was performed in HEK- 293 cells after transient knockdown of either RBM10 or Star- PAP. RNA was pulled down using  anti-StarPAP antibody or anti-IgG as mentioned in the protocol.

first: Ganesh

middle: R

last: Koshre

first: Nimmy

last: Mohan

first: Feba

last: Shaji

first: K

middle: M

last: Neeraja

first: Ali

last: Jamshaid


title: Systematic identification and characterization of uncharacterized transcription factors in Escherichia coli K-12 MG1655

first: Ye

last: Gao

address: 9500 Gilman Dr.

institute: UCSD

summary: Bacteria regulate gene expression to adapt to changing environments through transcriptional regulatory networks (TRNs). Although extensively studied, TRNs are not fully characterized since we do not know the identity of all the transcriptional regulators that comprise a TRN. Here, we experimentally evaluate 40 uncharacterized proteins in the model organisms Escherichia coli K-12 MG1655, which were previously predicted to be transcription factors (TFs). First, we used myc-tagging and a multiplexed ChIP-exo assay to characterize genome-wide binding sites for the 40 candidate TFs. Then, we compared those binding sites with those of RNA polymerase and sigma factors to increase the confidence in the measured DNA-binding events. Finally, we used these data to infer potential functional annotation for 13 candidate TFs. As a result, we characterized 570 new binding sites for 34 of 40 candidate TFs. Taken together, the study; 1) expands the number of confirmed TFs from 249 to 278, that is close to the estimated total of about 280 TFs in E. coli K-12 MG1655, 2) it provides a roadmap for  functional characterization of the 34 discovered TFs, and 3) it enables the elucidation of the first comprehensive TRN.

overall_design: Expression profiling data for wild type E. coli and their yTFs deletion strains were generated by RNA-seq, in duplicate

first: Bernhard

middle: O

last: Palsson


title: Epigenetic profiling and response to CD19 chimeric antigen receptor (CAR) T-cell therapy in B-cell malignancies

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

summary: Chimeric antigen receptor (CAR) T-cells directed against CD19 (CART19) are effective in relapsed/refractory (R/R) B-cell malignancies. Not all patients show treatment efficacy, but little is known about the molecular factors predicting clinical outcome of CART19 therapy. Our objective was to determine the effect of epigenetic changes in CART19 cells on the clinical course of B-cell malignancy patients treated with adoptive therapy. We report a case series of B-cell malignancy patients (68 males (M) and 46 females (F); median age of 24 years (range 3-70 years)), comprising 77 acute lymphoblastic leukemia (ALL) cases and 37 non-Hodgkin lymphoma (NHL) cases, who were treated with CART19 cells. Using a DNA methylation microarray, we determined the epigenomic changes that occur in the patient T-cells upon transduction of the CAR vector. We identified 984 genomic sites with differential DNA methylation between CAR-untransduced (UT) and CAR-transduced (TD) T-cells before infusion into the patient. 18 of these distinct epigenetic loci were significantly associated with complete response (CR). Using the sites linked to CR, the EPICART signature was established, which was associated with enhanced overall survival (OS).

overall_design:
The DNA methylation status of the CART19 transduced T-cells from 114 patients was established using the Infinium MethylationEPIC Array following the manufacturer’s instructions for the automated processing of arrays with a liquid handler (Illumina Infinium HD Methylation Assay Experienced User Card, Automated Protocol 15019521 v01). Raw signal intensity data were initially QC’d and preprocessed from resulting idat files using minfi Bioconductor package (v1.36.0). EPICART DNA methylation signature was obtained using a trained supervised classification model based on ridge regularized logistic regression. The classification model was optimized by tuning parameters with 10-fold cross-validation repeated three times using caret CRAN package (v6.0-86). All analyses were performed under R statistical environment (v4.0.3).

>>>Submitter states: IDAT files were not being provided due to privacy issues (idat files include SNPs that can be used to identify patients)<<<

first: Carlos

middle: A

last: Garcia-Prieto


title: Fibroblast growth factor receptor 3 in hepatocytes protects from liver injury and fibrosis

city: Zurich

first: Sabine

last: Werner

address: Otto-Stern-Weg 7

department: Department of Biology

country: Switzerland

institute: ETH Zurich

summary: ABSTRACT. The liver has a remarkable regenerative capacity, which is orchestrated by several growth factors and cytokines. We generated mice lacking Fgfr3 in hepatocytes and found increased liver injury and enhanced fibrosis in these animals. To unravel the underlying mechanisms we sequenced the RNA from isolated hepatocytes of Fgfr3 knockout and control mice and identifed differentially expressed genes involved in metabolic regulation, immune regulation and fibrosis.

overall_design: Alb-Cre mice and mice lacking Fgfr3 (Alb-R3) specifically in hepatocytes, were subjected to CCl4 or oil treatment for 48 hours and gene expression profiling was determined using RNA-seq

first: Abbie

middle: E

last: Fearon

first: Coenraad

middle: F

last: Slabber

first: Andrii

last: Kuklin


title: RNA sequencing data for hypoxic and normoxic vessels

city: New Haven

first: Edward

middle: Paul

last: Manning

state: CT

address: TAC 440 South, 300 Cedar St

institute: Yale School of Medicine, West Haven VA

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of mouse pulmonary arteries (main, right and left extralobar branches) from C57BL/6 mice exposed to 6 weeks or hypoxia (FiO2 10%) and normoxia (FiO2%)

overall_design: adult male mice (C57BL/6J; 14 weeks old, Jackson Laboratory, Bar Harbor, ME) were housed in an antigen-free and virus-free animal care facility under a 12-hour light and dark cycle. Two mice were exposed to hypoxic conditions by placing them in a plexiglass chamber connected to OxyCycler Models A420OC and AT42CO gas controllers and analyzers (BioSpherix, NY, USA). This gas control delivery system regulated the flow of room air, N2, and O2 into the chamber to create and maintain prescribed fraction inspired O2 (FiO2) levels. Persistent hypoxia defined by a FiO2 of 10% was maintained for 6 weeks at 24 hours/day. mice were fed a standard rodent chow and had free access to water. Animals were euthanized with overdose of urethane by intraperitoneal injection followed by exsanguination, followed by harvest of the pulmonary arteries.

middle: P

first: Abhay

middle: B

last: Ramachandra

first: Jonas

middle: C

last: Schupp

first: George

last: Tellides

first: Naftali

last: Kaminski

first: Jay

middle: D

last: Humphrey


title: Bone marrow regulatory T cells are a unique population, supported by niche-specific cytokines and plasmacytoid dendritic cells, and required for chronic graft-vs-host disease control

status: Public on Aug 21 2021

city: Brisbane

first: Dylan

middle: Patrick

last: Carter-Cusack

state: Queensland

address: 300 Herston Rd

department: Department of Immunology

country: Australia

institute: QIMR Berghofer Medical Research Institute

summary: RNASeq profiling shows signficant transcriptional differences between Treg isolated from the spleen and bone marrow compartments

overall_design: Transcriptional profile of Tregs from bone marrow and spleen

first: Kelli

last: MacDonald

first: Susan

middle: K

last: Nilsson


title: Stage-resolved genome architecture maps throughout meiotic prophase link regional variations in chromosome organization with homolog alignment

city: Shanghai

first: Qian

last: Bian

state: Shanghai

address: Pudong New District, Jinzun Rd, No.115

department: Ninth People’s Hospital

institute: Shanghai Jiao Tong University School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: During meiosis, chromosomes undergo extensive changes in structure and intranuclear positioning. How these chromosome organization changes occur and how they influence meiosis-specific chromosome events are not fully understood. Using Hi-C, we characterized chromosome architecture throughout mouse spermatogenesis at high temporal resolution. Our study revealed an intimate link between chromosome organization features and homolog pairing and alignment. We found that the meiotic chromosomes progressively reshape from TAD-like domains into linearly arranged loop arrays during prophase I. The transcriptionally active and inactive genomic regions exhibit distinct dynamics of loop growth, resulting in alternating domains consisting of shorter and longer chromosome loops. Such a domanial organization along meiotic chromosome axes is tightly correlated with the strength and precision of inter-homolog alignment. We further showed that a significant fraction of chromosomes near chromosome ends exhibit elevated inter-chromosomal association upon entering zygotene stage, while also exhibiting a higher degree of inter-homolog alignment. Using a mouse model defective in LINC complex component SUN1, we demonstrated that the prominent alignment of chromosome ends is dependent on the association of telomeres with the mechano-transducing LINC complex, but not the tethering of telomeres to the nuclear periphery. Taken together, our results suggest the 3D chromosome organization may provide a structural framework for the regulation of meiotic chromosome processes in higher eukaryotes.

overall_design: In this study, we employed mouse spermatogenesis as a model system to investigate the spatial organization of mammalian meiotic chromosomes. By combining fluorescence-activated cell sorting (FACS) and spermatogenesis synchronization, we generated a complete roadmap of meiotic chromosome architecture throughout the meiotic prophase I.

first: Wu

last: Zuo


title: Myeloid cell-based delivery of IFN-γ reprograms leukemia microenvironment and induces anti-tumoral immune responses

city: Milano

first: Matteo

last: Barcella

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

summary: The immunosuppressive microenvironment surrounding tumor cells represents a key cause of treatment failure. Therefore, immunotherapies aimed at reprogramming the immune system have largely spread in the past years. We employed gene transfer into hematopoietic stem and progenitor cells to selectively express anti-tumoral cytokines in tumor-infiltrating monocytes/macrophages. We show that Interferon-γ (IFNγ) reduced tumor progression in mouse models of B-cell acute lymphoblastic leukemia (B-ALL) and colorectal carcinoma (MC38). Its activity was dependent on the capacity of the immune system to respond to IFNγ and drove counter-selection of leukemia cells expressing surrogate antigens. Gene-based IFNγ delivery induced antigen presentation in the myeloid compartment and on leukemia cells, leading to a wave of T cell recruitment and activation, with enhanced clonal expansion of cytotoxic CD8+ T lymphocytes. The activity of IFNγ was further enhanced by either co-delivery of tumor necrosis factor α (TNFα) or by drugs blocking immunosuppressive escape pathways, with the potential to obtain durable responses.

overall_design: We undertook an unbiased transcriptional characterization of the B-ALL immune microenvironment performing 10x single cell RNA sequencing (scRNAseq) on total BM cells from mice treated or not with IFNγ gene therapy

first: Adele

last: Mucci

first: Gabriele

last: Antonarelli

first: Carolina

last: Caserta

first: Ivan

last: Merelli

first: Bernhard

last: Gentner


title: Stage-resolved genome architecture maps throughout meiotic prophase link regional variations in chromosome organization with homolog alignment (Hi-C, Cut&Tag, RNA-seq)


title: The Effects of avb3 Integrin Signaling on the Transcriptome of an Immortalized Line of Human Trabecular Meshwork Cells (TM-1)

status: Public on Aug 24 2021

city: MADISON

first: Donna

last: Peters

state: WI- WISCONSIN

address: 1300 UNIVERSITY AVE

department: Pathology & Laboratory Medicine

institute: UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE

summary:
Purpose: To study the effects of overexpressing either a wild type (WT) or a constitutively active (CA) avb3 integrin on the transcriptome of an immortalied line of human trabecular meshwork cells.
Methods: RNA was collected from four samples each of control cells expressing an empty vector (EV), cells overexpressing a WT avb3 integrin (WTb3) or a CA avb3 (CAb3) integrin. All cells had been cultured at confluence for 24 hr in 1%FBS-containing medium. RNA libraries were prepared using 1µg of RNA/sample with the TruSeq RNA sample preparation kit and sequenced on four lanes of an Illumina HiSeq 2500 System. Quality control was performed on the sequencing reads using fastq and skewer trimming software was used to preprocess raw fastq files. A quality control pipeline was then applied and each RNA-Seq sample was subsequently normalized by the method of trimmed mean M-values prior to DGE analysis using EdgeR.
Results: 5,186 genes had significantly altered expression (p<0.05) in WTb3 cells compared to EV cells (2,645 upregulated vs 2541 downregulated); 8,249 genes had significantly altered expression (p<0.05) in CAb3 cells compared to EV cells (4,094 upregulated vs 4,255 downregulated). However, 6,999 genes had significantly altered expression (p<0.05) in WTb3 cells vs CAb3 cells (3,524 upregulated vs 3,475 downregulated).
Conclusions: Overexpressing of both a WT avb3 and a constitutively active avb3 integrin caused signficant alterations in the transcriptome of immortalized TM-1 cells, however constitutive activation of avb3 signaling had a more pronounced effect on the TM-1 transcriptome than did mere overexpression of the integrin.

overall_design: Transcriptomes of immortalized trabecular meshwork cells overexpressing a wild type avb3 integrin and a constitutivelyl active avb3 integrin were compared using RNA-seq analysis.

first: Mark

last: Filla


title: Transcriptional profile of BRON mutant

city: Ames

first: Natalie

last: Clark

state: IA

address: Advanced Teaching and Research Building 2213 Pammel Drive

department: Plant Pathology and Microbiology

institute: Iowa State University

summary: We identified BRONTOSAURS (BRON) as a novel gene regulating BR response in the root. To determine transcripts differentially regulated by BRON, we performed RNASeq on the bron-2 mutant root and compared differentially expressed transcripts versus a wild type control.

overall_design: RNA was extracted from five-day old roots of wild type and bron-2 mutant plants and sequenced. Three biological replicates were collected for both wild type and mutant samples.

first: Rosangela

last: Sozzani


title: A single cell transcriptomic atlas identifies synapse-associated microglia in the developing zebrafish (bulk cells)

city: San Francisco

first: Leah

last: Dorman

address: 499 Illinois St

department: Data Science

institute: CZBiohub

summary: This study profiles developing and adult zebrafish macrophages and defines regional and functional microglial subtypes.

overall_design: Macrophages (Mpeg+ and CD45+ cells) were sorted and sequenced  from 28 dpf and 6 mpf zebrafish

first: Nick

last: Silva

first: Ilia

last: Vainchtein

first: Anna

last: Molofsky


title: The chromatin remodeler Ino80 mediates alternative RNAPII pausing site determination

status: Public on Aug 20 2021

city: Daejeon

first: Youngseo

last: Cheon

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: Promoter-proximal pausing of RNAPII is a critical step in early transcription elongation to precisely regulate gene expression. Here, we observed evidence of promoter-proximal pausing like distributions of RNAPII in S. cerevisiae. We find that Ino80p loss caused the transition of RNAPII pausing to the alternative pausing site at which is tightly associated with the +1 nucleosome. These Ino80p dependent genes showed better nucleosome positioning around the main pausing site which suggested the regulation of RNAPII pausing by Ino80p in a nucleosome context-dependent manner. Furthermore, we examined the similar INO80 dependent RNAPII pausing site determination in mESCs. Altogether, we hypothesize a highly conserved role of the chromatin remodeling Ino80 complex in controlling the early RNAPII elongation to establish intact pausing in various organisms, from budding yeast to mouse.

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Mus musculus

overall_design: For S. cerevisiae: PRO-seq and PRO-cap libraries that were generated in Ino80p-AID cells and various deletion mutants. A fixed amount of S. pombe cells were used for spike-in control. For mouse embryonic stem cells (mESCs): PRO-seq libraries that were generated in mESCs transfected with either siEGFP or siINO80.

first: Sungwook

last: Han

first: Daeyoup

last: Lee


title: CD45+ immune cells from mouse cochlea

status: Public on Aug 19 2021

city: Tel Aviv

first: Eldad

middle: David

last: Shulman

address: Kelechkin 35

country: Israel

institute: Tel Aviv University

summary: We sought to directly measure the molecular response in the cochlear immune cells following noise exposure.

overall_design: Cochleae were obtained at three time points after noise exposure (3, 7, and 14 days) to document both the acute and convalescent immune response, as well as from control untreated mice. Flow cytometry was used to select CD45+ immune cells for scRNA-seq analysis.

first: Barbara

last: Canlon

first: Christopher

last: Cederroth

first: Heela

last: Sarlus


title: Time course of brassinolide treatment on Arabidopsis seedlings

summary: Brassinosterioids (BRs) are plant hormones known to regulate many processes such as growth and development. However, how plants respond termporally BR signaling is not as well understaood. Thus, the goal of this study was to determine the temporal transcriptional changes in Arabidopsis seedlings treated with brassinolide. We determined differentially expressed genes at each time point to see how the plant response to BR evolves over time.

overall_design: 7-day old seedlings were treated with brassinolide (BL) at various time points. RNA was extracted from treated and mock seedlings at each time point, then sequenced using QuantSeq.

first: Trevor

last: Nolan

first: Justin

middle: W

last: Walley

first: Yanhai

last: Yin


title: Five-year-old 'Wink' grape cultivar

city: Nanjing

first: Chen

last: Wang

address: Weigang 1 Hao

institute: Nanjing Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: microRNAs(miRNAs) play critical regulatory roles mainly through cleaving targeted mRNAs or repressing gene translation during plant developments. Grapevine is amongst the most economically important fruit crops with whole genome available, and the study on grapevine miRNAs (Vv-miRNAs) have also been emphasized. However, the regulation mode of Vv-miRNAs on their target mRNAs during grapevine development has not been studied well, especially on a transcriptome-wide level. Here, six small RNA (sRNA) and mRNA libraries from various grapevine tissues were constructed for Illumina and Degradome sequencing. Subsequently, the spatiotemporal variation in the Vv-miRNAs’ regulation on their target genes was systematically analyzed. Totally, 242 known and 132 novel Vv-miRNAs were identified, and 193 target mRNAs including 103 for known and 90 for novel miRNAs were validated in one or more of tissues examined. The interesting finding was that over 50% of novel miRNAs were expressed exclusively in flowers or berries where they had tissue-specific cleavage roles on their target genes, especially, the breadth of their cleavage sites in flower tissues. Moreover, six novel miRNAs in berries were found to response to exogenous gibberellin (GA) and/or ethylene by real time RT-PCR (qRT-PCR) analysis, confirming their regulatory functions during berry development. Other finding was that about 93.6% of the known miRNAs possessed the high conservation in various tissues where their expression levels exhibited some dynamic variations during grapevine development. Significantly, it was found the phenomena that some Vv-miRNA families exist one key member that act as the main regulator of their target genes during grapevine development.

overall_design: young berry (5 days after flower), stone-hardening stage berry  (45 days after flower) and mature berry (90 days after flower) of grapevine were selected, and these samples can be extracted total RNA, and then were separated to small RNAs used for Solexa sequencing, respectively. Subsequenctly, we carried out the analysis of Solexa sequencing data, and performed the research on the dynamic variations of  regulatory modes of grapevine miRNAs on their target genes during grapevine development process at the whole transcriptome level.

first: Jinggui

last: Fang


title: A single cell transcriptomic atlas identifies synapse-associated microglia in the developing zebrafish (single cells)


title: Retinoic acid receptors and the control of positional information in the regenerating axolotl limb

city: Gainesville

first: Malcolm

last: Maden

state: Florida

department: Biology

institute: University of Florida

summary: We know little about the control of positional information (PI) during axolotl limb regeneration which ensures that the limb regenerates exactly what was amputated and the work reported here investigates this phenomenon. Retinoic acid administration changes the PI in a proximal direction so that a complete limb can be regenerated from a hand. Rather that identifying all the genes altered by RA treatment of the limb, we have eliminated many off-target effects by using retinoic acid receptor selective agonists. We firstly identify the receptor involved in this respecification process as RARα and secondly identify the genes involved by RNA sequencing of the RARα-treated blastemal mesenchyme. We find 1177 up-regulated genes and 1403 down-regulated genes which could be identified using the axolotl genome. These include several genes known to be involved in retinoic acid metabolism and in patterning. Since positional in-formation is thought to be a property of the cell surface of blastemal cells when we examine our dataset with an emphasis on this aspect, we find the top canonical pathway is integrin signaling. In the extracellular matrix compartment, we find an MMP and several collagens are up-regulated and several cell membrane genes and secretory factors are also up-regulated. This provides data for future testing of the function of these candidates in the control of PI during limb regeneration.

overall_design: Gene expression analysis of axolotl forelimb blastema mesenchyme tissue following 25 nM systemic Am580 treatment

first: Trey

last: Polvadore


title: Single cell sequencing of human intestinal organoid cells.

status: Public on Aug 17 2021

city: Utrecht

first: Jens

last: Puschhof

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Unbiased and FACS was performed on human intestinal organoid cells and coupled to single cell sorting by the SortSeq protocol (Muraro et al., 2016).

overall_design: Intestinal organoid  differentiation was induced through addition of ER+BMP differentiation medium. After 5 days of differentiation, cells were collected by FACS and subjected to single cell RNA sequencing.

first: Joep

last: Beumer

first: Maarten

middle: H

last: Geurts

first: Mart

last: Lamers

first: Jingshu

last: Zhang

first: Jelte

last: van der Vaart

middle: Z

last: Mykytyn

first: Tim

middle: I

last: Breugem

first: Samra

last: Riesebosch

first: Debby

last: Schipper

first: Petra

last: van den Doel

first: Wim

last: de Lau

first: Cayetano

last: Pleguezuelos-Manzano

first: Georg

last: Busslinger

first: Bart

middle: L

last: Haagmans

first: Hans

last: Clevers


title: Next Generation Sequencing Facilitates Quantitative Analysis of Uncut and Injured Larval Zebrafish Fin Fold Transcriptomes

city: Hsinchu

first: Yi-Fan

last: Lin

address: 101 Sec.2, Kuang-Fu Rd.

country: Taiwan

institute: National Tsing-Hua University

summary: We report increased expression of mitochondrial biogenesis genes in regnerating larval fin fold

overall_design: Larval fin fold mRNA profiles of 3-day old control and fin amputated zebrafish

first: Jessica

last: Sam

first: Todd

last: Evans


title: The alteration of circulating exosomal mRNAs in acute myocardial infarction is associated with inflammation response

city: Guangzhou

first: guodong

last: he

address: zhongshan road No.102

institute: Guangdong Provincial People's Hospital

summary: Background: Although many cardiovascular disease studies have focused on the characteristics of microRNAs in circulating exosomes, the profile and the potential clinical diagnostic value of plasma exosomal long RNAs (exoLRs) in acute myocardial infarction (AMI) is still unknown. Methods: In this study, exoLRs profile of 10 AMI patients, 8 stable coronary artery disease (CAD) patients, and 10 healthy individuals were achieved by exosomes isolation and RNA sequencing. Bioinformatics approaches were used to investigate the features and potential clinical value of exoLRs. Results: Exosomal messenger RNAs (mRNAs) made up a majority of the total exoLRs. Immune cell types analyzed by CIBERSORT showed that neutrophils and monocytes were significantly enriched in the AMI group which were consistent with the clinical baseline characteristic. The biological processes enrichment analyses of different exosomal mRNAs and co-expression network analysis both indicated that neutrophils activation associated processes were enriched in the AMI group. We further identified two exosomal mRNA ALPL and CXCR2 which might be served as potential biomarkers for AMI diagnosis. Conclusions: Our study explored the alteration of exoLRs in the AMI patients which was associated with the acute inflammatory response mediated by neutrophils. Exosomal mRNAs ALPL and CXCR2 might be potentially useful for AMI diagnosis.

overall_design: In this study, we explored the plasma exoLRs profile of 10 AMI, 8 stable coronary artery disease (CAD), and 10 healthy individuals by RNA sequencing analyses to investigate its features and potential diagnostic value in clinical.

first: Guodong

last: He

first: Yuqing

last: Huang

first: Lin

last: Liu

first: Jiayi

first: Kenneth

last: Lo

first: Yuling

last: Yu

first: Chaolei

last: Chen

first: Bin

first: Yingqing

last: Feng


title: Elevated Asparagine Biosynthesis Drives Brain Tumor Stem Cell Metabolic Plasticity and Resistance to Oxidative Stress

status: Public on Aug 18 2021

city: West Hollywood

first: AGCT

last: Core

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

summary: Asparagine synthetase (ASNS) is a gene on the long arm of chromosome 7 that is copy number amplified in the majority of glioblastomas. ASNS copy number amplification is associated with a significantly decreased survival. Using patient-derived glioma stem cells (GSCs), we showed significant metabolic alterations occur in gliomas when perturbing the expression of asparagine synthetase, which is not merely restricted to amino acid homeostasis. ASNS-high GSCs maintained a slower basal metabolic profile yet readily shifted to a greatly increased capacity for glycolysis and oxidative phosphorylation when needed. This led ASNS-high cells to a greater ability to proliferate and spread into brain tissue. Finally, we demonstrate that these changes confer resistance to cellular stress, notably oxidative stress, through adaptive redox homeostasis which led to radiation resistance. Furthermore, ASNS overexpression led to modifications of the one-carbon metabolism to promote a more antioxidant tumor environment revealing a metabolic vulnerability that may be therapeutically exploited.

overall_design: RNA sequencing on glioma stem cells (ASNS-high and -low) underwent irradiation and cultured for 0, 3 and 14 days with control cells without irradiation.

first: Tom

middle: M

last: Thomas

first: Ken

last: Miyaguchi

first: Yizhou

last: Wang

first: John

middle: S


title: Differentially Expressed Genes in Wild-type Tobacco Leaves and NtCBL5A-OE Transgenic Tobacco Leaves Under Salt Stress

city: Qingdao

first: Qian

state: Shandong

address: Keyuanjingsi Road, Laoshan District

institute: Chinese Academy of Agricultural Sciences

summary:
Purpose: To further identify the genes and pathways involved in the necrotic phenotype of NtCBL5A-OE lines, the leaf transcriptome profiling of WT and OE-2 lines grown under control conditions and salt stress (100 mM NaCl) at 4 DAT were sequenced and compared.
Methods: Two datasets of differentially expressed genes (DEGs) were made in which we identified the genes that were differentially expressed as a result of the overexpression of NtCBL5A: Control-WT vs Control-OE2 (C-WT/C-OE2), Salt-WT vs Salt-OE2 (S-WT/S-OE2). Another two datasets were also used to identify the transcripts that were responsive to the salt treatments: Control-WT vs Salt-WT (C-WT/S-WT) and Control-OE2 vs Salt-OE2 (C-OE2/S-OE2). DEGs from C-WT/C-OE2 and S-WT/S-OE2 were compared to select the transcripts affected by NtCBL5A overexpression only under salt stress. We also compared DEGs from C-WT/S-WT and C-OE2/S-OE2 to identify the specific transcripts affected by salt stress and only in NtCBL5A-OE lines. This procedure was done for two independent experiments, and only DEGs that were identified in both experiments were considered.
Results: The OE-affected DEGs and salt-affected DEGs together resulted in 2079 up-regulated DEGs and 1154 down-regulated DEGs, strongly affected by the combination of NtCBL5A overexpression and salt stress.

overall_design: Tobacco leaf mRNA profiles of 4 days after salt treatment (100 mM NaCl in hydropoic system) in wild type (WT) and NtCBL5A-OE lines

first: Jingjing

last: Mao

first: Jiaping

last: Yuan

first: Zhijie

last: Mo

first: Lulu

last: An

first: Sujuan

last: Shi

first: Richard

middle: G

last: Visser

last: Bai

first: Yuhe

last: Sun

first: Guanshan

first: Haobao

first: C

last: van der Linden


title: Next Generation Sequencing of Transcriptomes of WT and Transgenic Treg cells to differentiate effect of TIM-3 on Tregulatory cell geneexpression.

status: Public on Aug 16 2021

city: Pittsburgh

first: Uma

last: Chandran

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

summary: Significant differences were found in transcriptional profiles of WT and TIM-3+(GFPHi and GFP Low) cells, suggesting major shifts in metabolic status, cytokine profiles and suppresive capacity of Tregulatory cells due to expression of TIM-3 in Tregulatory cells.

overall_design: WT and TIM-3+(GFPHi and GFP Low) cells

first: Hridesh

last: Banerjee

first: Larry

last: Kane

first: Alexander

last: Chang


title: Lysyl hydroxylase 1 deficiency exacerbates the alterations of gene transcriptional profile of abdominal aorta in angiotensin II induced abdominal aortic aneurysm

status: Public on Aug 15 2021

city: Peking

first: Zhengqin

last: Rong

address: Beiqing Road

institute: Basepedia

summary: Lysyl hydroxylase 1 (LH1) plays an important role in hydroxylation of lysyl residuel in Xaa-Lys-Gly. The hydroxylysine residues serve as sites of attachment for carbohydrate units which are essential for the formation of intra- and intermolecular collagen crosslinks. To gain mechanistic insights into the effects of LH1 deficiency on abdominal aortic aneurysm (AAA) formation, a whole transcriptomic analysis of abdominal aorta were performed using RNA-seq. The abdominal aorta of mice for RNA-seq were acquired at day 14 after angiotensin II infusion in order to provide the mechanistic or causal evidence of a direct participatory role of LH1 to the effects of AAA.

overall_design: 20 samples. There are 4 groups: WT-Saline group, wild-type mice on C57BL/6 background were infused with saline by implanting osmotic pumps subcutaneously for 14 days. WT-AngII group, wild-type mice on C57BL/6 background were infused with angiotensin II (1000 ng/kg per minute) by implanting osmotic pumps subcutaneously for 14 days. LH1 KO-Saline group, LH1 knock-out mice on C57BL/6 background were infused with saline by implanting osmotic pumps subcutaneously for 14 days. LH1 knock-out-AngII group, LH1 knock-out mice on C57BL/6 background were infused with angiotensin II (1000 ng/kg per minute) by implanting osmotic pumps subcutaneously for 14 days.

first: Hao

last: Li

first: Hao-chen

last: Xu


title: A PTEN variant uncouples longevity from impaired fitness in C. elegans via tuning the activity of FOXO and NRF

status: Public on Aug 13 2021

first: Seung-Jae

middle: V

last: Lee

address: 291 Daehak-ro

department: Biological Sciences

institute: KAIST

summary: Insulin/IGF-1 signaling (IIS) regulates various physiological aspects in many species. In C. elegans, mutations in daf-2/insulin/IGF-1 receptor dramatically increase lifespan and pathogen resistance, but generally impair motility, development, and reproduction. Whether these pleiotropic effects can be dissociated at a specific step in the IIS pathway remains unknown. Here we show that a single amino acid change in DAF-18, PTEN phosphatase, allows worms to maintain longevity and enhanced immunity in daf-2 mutants compared to wild-type, without defects in growth and motility. Through performing a mutagenesis screen, we identified a missense mutation in daf-18 [daf-18(yh1)], which suppressed developmental defects in daf-2 mutants with small effects on pathogen resistance. We showed that the daf-18(yh1) caused a reduction in its function, but maintained long lifespan, motility span, and resistance against various stresses in daf-2 mutants. We further showed that daf-18(yh1) retained the activity of DAF-16/FOXO but restricted detrimental upregulation of SKN-1/NRF, for exerting beneficial physiological consequences. Our study will provide important insights into how one evolutionarily conserved component, PTEN coordinates healthy longevity and fitness.

overall_design: Four samples each of daf-2(e1370), daf-2(e1370); daf-18(yh1), and daf-2(e1370); daf-18(nr2037) mutants

first: Hae-Eun

last: Park

first: Wooseon

last: Hwang

first: Seokjin

last: Ham


title: Bulk RNA sequencing of human intestinal and airway organoids

first: Jelte

last: van der Vaart

address: Universiteitsweg 100

department: Center for Molecular Medicine

institute: University Medical Center Utrecht

summary: Bulk RNA sequencing was performed on intestinal and airway organoids. Also airway organoid derived air-liquid interface cultures were sequenced

overall_design: RNA was extracted from intestinal organoids that were either grown in expansion conditions (EXP) or differentiation conditions (DIF). Airway organoids were grown in expansion medium (EM) or differentiated in differentiation medium (DM). Air-liquid interface cultures of trachea, bronchus and bronchiole were derived from airway organoids of that airway section.

first: Joep

last: Beumer

first: Maarten

last: Geurts

first: Mart

last: Lamers

first: Jens

last: Puschhof

first: Jingshu

last: Zhang

first: Anna

last: Mykytyn

first: Tim

last: Breugem

first: Samra

last: Riesebosch

first: Debby

last: Schipper

first: Petra

last: van den Doel

first: Wim

last: de Lau

first: Cayetano

last: Pleguezuelos-Manzano

first: Georg

last: Busslinger

first: Bart

last: Haagmans

first: Hans

last: Clevers


title: ChIP-exo analysis reveals novel uncharacterized transcription factors involved in the diverse regulatory functions of Escherichia coli

city: La Jolla

first: Ye

last: Gao

address: 9500 Gilman Dr.

institute: UCSD

summary: Bacteria regulate gene expression to adapt to changing environments through transcriptional regulatory networks (TRNs). Although extensively studied, TRNs are not fully characterized since the identity of all the transcriptional regulators that comprise a TRN are not known. Here, we experimentally evaluate 40 uncharacterized proteins in the model organism Escherichia coli K-12 MG1655, which were previously predicted to be transcription factors (TFs). First, we used myc-tagging and a multiplexed ChIP-exo assay to characterize genome-wide binding sites for these candidate TFs. We then compared those binding sites with those of RNA polymerase and sigma factors to increase the confidence in the measured DNA-binding events. Finally, we used these data to infer potential functional annotations for 13 candidate TFs. Our results revealed that these candidate TFs have a varied number of regulatory genes and are involved in E. coli’s primary cellular processes. Taken together, thes results: (1) expand the number of confirmed TFs from 249 to 276, close to the estimated total of 280 TFs in E. coli K-12 MG1655; (2) provide a roadmap for the functional characterization of the newly discovered TFs; and (3) enable the elucidation of the first comprehensive TRN in this model organism.

overall_design: Identification of genome-wide bindings for uncharacterized transcription factors in E. coli K-12 MG1655, using ChIP-exo technology

first: Bernhard

last: Palsson


title: Enhancer binding of RUNX1 and Groucho family repressor TLE3 is stabilized by FOXC1 to block differentiation in acute myeloid leukemia [ChIP-Seq]

city: Manchester

last: Somervaille

address: Wilmslow Rd

department: Manchester Institute

country: United Kingdom

institute: Cancer Research UK

summary: A differentiation block is the cardinal pathologic feature of acute myeloid leukaemia (AML) but the underlying mechanisms are incompletely understood. Despite absent expression in normal hematopoietic lineages, the Forkhead family transcription factor FOXC1, which is a critical regulator of normal mesenchymal and mesodermal differentiation, is highly expressed in ~20% of cases of AML where it confers a block to monocyte/macrophage lineage differentiation. Through integrated proteomics and bioinformatics approaches, we discovered that FOXC1 interacts with RUNX1 through its Forkhead DNA binding domain and that the two factors co-occupy a discrete set of primed or active enhancers distributed close to monocyte/macrophage differentiation genes. FOXC1 stabilises association of RUNX1, HDAC1 and the Groucho family repressor protein TLE3 at these sites. FOXC1 knockdown induced loss of these repressor proteins and gain of CEBPA binding, with localised increase in enhancer acetylation; nearby genes, including KLF2, were up regulated. A genome-wide redistribution of RUNX1 and TLE3 binding from enhancers to promoters was triggered by FOXC1 knockdown leading to repression of self-renewal genes including MYC and MYB. Thus, FOXC1 misexpression confers a differentiation block in AML by stabilising recruitment of a RUNX1/HDAC1/TLE3 repressor complex at primed or active enhancers close to genes which control monocyte/macrophage lineage differentiation.

overall_design: Human Fujioka AML cells were infected with a lentivirus targeting FOXC1 for KD or a non-targeting control (NTC). Primary human AML cells were obtained from the Manchester Cancer Research Centre Tissue Biobank (approved by the South Manchester Research Ethics Committee). The Biobank archive was searched for samples from patients with high expression of FOXC1 and sufficient viable cells from ChIP sequencing.


title: Transcriptional response in the heart after low-dose gamma

city: St. Louis

first: Jeffrey

last: Szymanski

email: jeszyman@gmail.com, szymanski@wustl.edu

state: Missouri

address: 4511 Forest Park

institute: Washington University in Saint Louis

summary: We report whole transcriptome sequencing of the intraventricular septum of mouse heart 2 and 6 weeks after 25 Gy ionizing radiation.   The objective of this experiment was to identify genes and pathways differentially regulated by ionizing radiation in the heart. Image-guided isocentric gamma irradiation was delivered to experimental groups under isoflurane anesthesia in a single, 25 Gy dose over approximately 15 minutes. Control group animals were experimental group littermates which received anesthesia and CT imaging but no radiation. RNA was isolated from intraventricular septum using TRIzol.

overall_design: Whole transcriptome profiles of mouse heart intraventricular septum after 25 Gy single dose ionizing radiation. Three groups of n=6 per group: a normal reference control (ctrl), 2 weeks post irradiation (2wk), and 6 weeks post irradiation (6wk)

first: Stacey

last: Rentschler


title: Characterizing Epigenetic Changes in Methylation Mutants (elp2-5 and met1-7) in Response to Spaceflight.

first: Robert

middle: J.

last: Ferl

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

type: Methylation profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: MACE Sequencing of MLL-AF4 KD PDX cells

city: Munich

first: Irmela

last: Jeremias

address: Feodor-Lynenstr. 21

institute: Helmholtz Zentrum München, German Center for Environmental Health (HMGU)

summary: MACE sequencing of MLL-AF4 KD and control PDX cells out of an inducible knockdown in vivo experiment showed a specific change in the gene expression profile to leukemic patient without MLL rearrangement pointing out the specificity of the shRNA system.

overall_design:
MLL-AF4 KD and control PDX cells were isolated out of the murine bone marrow 28 days after induction of the shRNA expression by tamoxifen. Cells were analyzed by MACE sequencing to analyze the mRNA expression pattern.
[contributor] GenXPro GmbH

first: Kerstin

last: Völse

first: Alexander

last: Wilhelm


title: Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes

city: Basel

first: Grégoire

last: Vernaz

address: Vesalgasse 1

institute: University of Basel

summary: Whole-genome methylomes and total transcriptomes for muscle and liver tissues of Lake Malawi cichlid species characterised in the context of phenotypic diversification.

sample_organism:
Astatotilapia calliptera
Maylandia zebra
Diplotaxodon limnothrissa
Aulonocara stuartgranti
Pundamilia nyererei
Rhamphochromis longiceps
Petrotilapia genalutea

overall_design: Biological replicates (≥2) for all RNAseq and WGBS samples. Male, wild-caught samples for all Lake Malawi cichlid species analysed in this study.

first: Eric

middle: A

last: Miska


title: Characterizing Epigenetic Changes in Methylation Mutants (elp2-5 and met1-7) in Response to Spaceflight. [Bisulfite-Seq]

summary: Epigenetic changes in the DNA methylome are increasingly shown to play an integral role in regulating gene expression necessary for plants’ adaption to environmental stressors. Plants subjected to the novel environment of spaceflight onboard the International Space Station (ISS), show stress-related transcriptomic changes most notably associated with pathogen stress response. Here, we investigate how known terrestrial stress associated epigenetic modulations might play a role in spaceflight adaptation. To examine the role of 5mCyt in spaceflight adaptation, the APEX04-EPEX experiment conducted onboard the ISS evaluated the spaceflight altered genome wide methylation profiles of two methylation regulating gene mutants (methyltransferase 1 (met1-7) and elongator complex subunit 2 (elp2-5)) that are involved in pathogen defense response, along with a wild type Col-0 control. MethylSeq and RNAseq analyses were performed on both spaceflight grown samples and ground grown controls. In addition, the epigenetics effects that may contribute to the differential gene expression patterns observed between leaf and root tissues were also investigated in an organ-specific manner.

overall_design: Sterilized Arabidopsis thaliana seeds of the Columbia (Col-0), met1-7 or elp2-5 genotype were sown onto the surface of 100 mm2 square petri dishes containing a solid medium of 0.5% Phytagel™ /0.5x MS media and then wrapped in Duvetyne™ cloth. The plates were stored at 4°C and remained dormant until its installation into the Vegetable Production System (Veggie) hardware on the ISS and a comparable set installed into the Veggie hardware on the ISS Environmental Simulator (ISSES) chamber at Kennedy Space Center (KSC). These plates made up the NASA Advanced Plant Experiment 04 – Epigenetic Expression (APEX04-EPX) experiment that was launched on the SpaceX mission CRS-10. Plants in the Veggie hardware were exposed to constant light conditions of 100-135 µmoles/m2/s PAR and grown for eleven days before being harvested into Kennedy Space Center Fixation Tubes (KFTs) and fixed in RNAlater™ (Ambion, Grand Island, NY, USA). Samples from each plate were harvested into individual KFTs. The KFTs were then stowed at -80°C in the MELFI freezer aboard the ISS. The comparable ground control samples were also harvested into KFTs and stored in a standard -80°C freezer. All samples were kept frozen until delivery to the laboratory for analysis. Each plate was used as a biological replicate and a total of 4 replicates were used for the analyses. Leaf and root tissues from each sample were dissected using an Olympus microscope and materials from three individual plants per replicate were used for RNA extraction, whereas material from 10-12 plants were allocated for DNA extraction.

first: Natasha

middle: J

last: Sng

first: Mingqi

last: Zhou

first: Collin

last: LeFrois

first: Jordan

last: Callaham

first: Anna-Lisa

last: Paul


title: Characterizing Epigenetic Changes in Methylation Mutants (elp2-5 and met1-7) in Response to Spaceflight. [RNA-Seq]


title: Pathway Signatures Derived from On-treatment Tumor Specimens Predict Response to Anti-PD1 Blockade in Metastatic Melanoma

city: Philadelphia

first: Tian

last: Tian

address: 3615 Civic Center Blvd

department: Center of Applied Genomics

institute: Children's Hospital of Philadelphia

summary: Both genomic and transcriptomic signatures have been developed to predict responses of metastatic melanoma to immune checkpoint blockade (ICB) therapies; however, most of these signatures were derived from pre-treatment biopsy samples. Here, we developed pathway-based signatures that predict response of metastatic melanoma to anti-PD1-based therapies in four independent datasets with RNAseq and clinical response data available for both pre- and on-treatment metastatic melanomas. We first identified pathway signatures that were significantly enriched in tumor specimens from anti-PD1 responders (R) compared to non-responders (NR) at pre-treatment and on-treatment time points, respectively. We also identified pathway signatures that were differentially expressed in pre-treatment versus on-treatment samples derived from R. Finally, we interrogated the capacity of the two types of signatures in predicting response of metastatic melanoma to anti-PD1 therapies in comparison with existing gene expression signatures. And we also investigated the effect of biopsy sites at the same biopsy time point on predictive performance of response to anti-PD1 therapy. Overall, we demonstrate that pathway-based signatures derived from on-treatment tumor specimens are highly predictive of response to anti-PD1 blockade therapies in patients with metastatic melanoma.

overall_design: RNA was purified from patients' frozen or formalin-fixed tumor specimens and subject to quality control.  RNA samples of good quality were sequenced.

first: Zhang


title: 7SK-controlled RNA polymerase II pausing orchestrates gene transcription with splicing

status: Public on Aug 12 2021

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

summary: RNA polymerase (Pol) II promoter-proximal pausing is a common regulatory step to initiate RNA synthesis and it is coordinated by a ribonucleoprotein complex scaffolded containing the noncoding RNA Rn7sk. However, how this transcriptional mechanism modulates gene expression programs in adult tissues is largely unknown. Here, we released paused RNA Pol II by depleting Rn7sk during mouse and human epidermal stem cell differentiation. Unexpectedly, the forced release of transcription robustly repressed RNA levels including numerous cell cycle regulators leading to cell cycle exit and differentiation. The repression of genes occurred in the absence of chromatin remodelling at promoters and enhancers. Instead, it was caused by splicing defects and co-transcriptional RNA degradation. However, rather than acting globally, Rn7sk modulated transcription gene-specifically. Genes that required Rn7sk for efficient transcription contained highly accessible promoters, lower guanosine and cytosine (GC) content, shorter introns, and weaker 3’ splice sites. In the absence of a tightly controlled Pol II pause release complex, these intrinsic gene properties cumulated in impaired splicing leading to RNA decay. Thus, 7SK-regulated transcriptional pausing is an essential step to coordinate transcription with splicing to permit productive transcription of a distinct set of genes.

overall_design: Total and 4SU RNA-Seq of wild type and Rn7sk-/- human keratinocytes; with or without Pladienolide B treatment (1h, 4h, no); 4 replicates per condition.

first: Roberto

last: Bandiera

first: Susanne

last: Bornelöv

first: Michaela

last: Frye


title: Electrogenic Na+-coupled HCO3- cotransporter NBCe1 regulates pancreatic beta cell function in type 2 diabetes

status: Public on Aug 11 2021

city: Cambridge

first: Matthew

middle: R

last: Brown

state: MA

address: 75 Ames St

institute: Broad Institute

summary: Pancreatic beta cell failure in type 2 diabetes (T2DM) is attributed in part to perturbations of the beta cell's transcriptional landscape resulting in the aberrant regulation of glucose-stimulated insulin secretion. Recent studies identified SLC4A4 (a gene encoding an electrogenic Na+-coupled HCO3- cotransporter and intracellular pH regulator, NBCe1) as one of the mis-expressed genes in beta cells of patients with T2DM. Thus, in the current study we set out to test the hypothesis that mis-expression of SLC4A4/NBCe1 in T2DM beta cells contributes to beta cell dysfunction and impaired glucose homeostasis. To address this hypothesis, we first confirmed induction of SLC4A4/NBCe1 expression in beta cells of patients with T2DM and demonstrated that its expression is associated with loss of beta cell transcriptional identity, intracellular alkalinization, and beta cell dysfunction. In addition, we generated a beta cell selective Slc4a4/NBCe1 knockout mouse model and report that these mice are protected from diet-induced metabolic stress and beta cell failure. Importantly, improved glucose tolerance and enhanced beta cell function in Slc4a4/NBCe1 deficient mice was due to augmented mitochondrial function and increased expression of genes regulating beta cell identity and function. These results suggest that increased beta cell expression of SLC4A4/NBCe1 in T2DM plays a contributory role in promotion of beta cell failure and should be considered as a potential novel therapeutic target.

overall_design: 6 samples total were analyzed. 3 replicates for control (β-Slc4a4+/+) and 3 replicates for beta cell selective Slc4a4 knockout (β-Slc4a4-/-) islets following 8 weeks of 60% high fat diet

first: Heather

last: Holmes

first: Kuntol

last: Rakshit

first: Naureen

last: Javeed

first: Tracy

last: Her

first: Alison

last: Stiller

first: Satish

last: Sen

first: Gary

middle: E

last: Shull

first: Y

last: Prakash

first: Michael

middle: F

last: Romero

first: Aleksey

last: Matveyenko


title: Characterization of organ-specific regulatory B cells using single-cell RNA sequencing

city: Guang Zhou

first: Siyu

last: Yang

address: outer ring road 384

institute: South China University of Technology

summary: We characterized Breg cells by scRNA-seq based on the immunosuppressive gene expression profile and B10 related genes, and delineated their transcriptional profiles, underlying functions and BCR clonotypes in different mouse organs under physiological condition.

overall_design: B cells sorted from liver, spleen, mLN, BM and PC of four wild type mice

first: Si-Yu

first: Jie

last: Long

first: Meng-Xing

last: Huang

first: Pan-Yue

last: Luo


title: HIV reprograms host m6Am RNA methylome by viral Vpr protein-mediated degradation of PCIF1

status: Public on Aug 09 2021

city: La jolla

first: Qiong

last: Zhang

state: California

department: Pediatrics

summary: To identify m6Am genes that are responsible for HIV inhibition, m6Am-exo-seq was performed in control, PCIF1 KO T cells, and cells infected with HIV.

overall_design: m6Am-exo-seq was performed in control, PCIF1 KO Jurkat cells, or Jurkat cells infected with HIV LAI strain at an MOI of 4 for 3 days. m6Am genes were identified as 5'UTR methylated peaks that are decreased in PCIF1 cells

first: Yuqi

last: Kang


title: Enhancer binding of RUNX1 and Groucho family repressor TLE3 is stabilized by FOXC1 to block differentiation in acute myeloid leukemia [RNA-Seq]

first: Tim

middle: C

last: Somervaille

overall_design: Human Fujioka AML cells were infected with a lentivirus targeting FOXC1 for KD or a non-targeting control (NTC).


title: Atlas of Clinically Distinct Cell States and Cellular Ecosystems Across Human Solid Tumors

city: Stanford

first: Magdalena

last: Matusiak

address: 300 Pasteur Dr

department: Pathology

institute: Stanford University

summary: Determining how cells vary with their local signaling environment and organize into distinct cellular communities is critical for understanding processes as diverse as development, aging, and cancer. Here we introduce EcoTyper, a new machine learning framework for large-scale identification and validation of cell states and multicellular communities from bulk, single-cell, and spatially-resolved gene expression data. When applied to 12 major cell lineages across 16 types of human carcinoma, EcoTyper identified 69 transcriptionally-defined cell states. Most states were specific to neoplastic tissue, ubiquitous across tumor types, and significantly prognostic. By analyzing cell state co-occurrence patterns, we discovered 10 clinically-distinct multicellular communities with unexpectedly strong conservation, including four with unique myeloid and stromal elements, one enriched in normal tissue, and two associated with early cancer development. This study elucidates fundamental units of cellular organization in human carcinoma and provides a framework for large-scale profiling of cellular ecosystems in any tissue (https://ecotyper.stanford.edu).

overall_design:
6 samples from 3 patients, 2 replicates from patient nr 380, 1 replicate from patient nr 406, 3 replicates from patient nr 393
Submitter declares that the raw data will be deposited in dbGaP due to patient privacy concerns.'

first: Chunfang

last: Zhu

first: Matt

last: van de Rijn


title: Enhancer binding of RUNX1 and Groucho family repressor TLE3 is stabilized by FOXC1 to block differentiation in acute myeloid leukemia


title: RAC1 is an essential cofactor for estrogen receptor alpha

city: Miami

first: Jun

last: Sun

state: FL

department: Sylvester Comprehensive Cancer Center

institute: University of Miami


title: RAC1 is an essential cofactor for estrogen receptor alpha [ChIP-seq]

summary: We identified a small GTPase protein RAC1 as an intrinsic cofactor in the estrogen receptor alpha (ER) complex that is required for the function of ER.

overall_design: ChIP-seq analyses identified co-localizations of ER and RAC1 on chromatin in ER+ breast cancer cells. RNA-seq analyses were performed in MCF-7 cells after down-regulation of RAC1 using siRNA. Newly synthesized RNAs were analysed in MCF-7 cells after the cells were treated with estrogen in combination with RAC1 inhibitor EHT 1864.

first: Stephen

middle: D

last: Nimer

first: Marc

last: Lippman


title: Polymerase II pausing licenses cell-cycle progression (ChIP-Seq)

first: Sabine

last: Dietmann

summary: RNA polymerase II promoter-proximal pausing is orchestrated by a ribonucleoprotein complex scaffolded by the noncoding RNA Rn7sk. However, how this interruption of transcription is mechanistically linked to RNA production remains largely unknown. Here, we show that forcing the pause release by germ-line deletion of Rn7sk was embryonic lethal, yet conditional deletion of Rn7sk enhanced stem cell differentiation in skin. To explore the immediate transcriptional mechanisms underpinning enhanced differentiation, we metabolically labelled newly-synthesized RNAs after Rn7sk deletion. Unexpectedly, forced pause release robustly repressed transcription specifically at cell cycle regulators, in the absence of chromatin remodeling at promoters and enhancers. Our results indicate that polymerase pausing affords the core elongation machinery time to properly assemble, and forced elongation triggers splicing defects and nuclear RNA decay. Cell cycle regulators appear highly sensitive to mis-regulation of the elongation machinery due to unique genomic features of high promoter accessibility and low GC–content in the gene body. Transcriptional pausing thus serves as a rate-limiting step in controlling cell division.

overall_design: ChIP-Seq using 5μg of H3K4Me1 (Abcam) or 10μg of H3K27Ac (Abcam) or RNA Pol II N20 antibodies in Rn7sk KD keratinocytes

first: Roberto

last: Bandiera

first: Susanne

last: Bornelov

last: Dietman

first: Michaela

last: Frye


title: Polymerase II pausing licenses cell-cycle progression (RNA-Seq)

overall_design: Cells were transfected with siRNAs, control or agains Rn7SK, using Lipofectamine RNAi and collected 24h or 48h later.


title: Polymerase II pausing licenses cell-cycle progression


title: Identification And Characterization Of Histone Mark Isonicotinylation That Is Induced By Anti-tuberculosis First-line Drug Isoniazid

city: Beijing

first: Hongquan

address: #38 Xue Yuan Road

department: Human Anatomy, Histology and Embryology

institute: Peking University

summary: We identified and characterized a previously undescribed histone mark, lysine isonicotinylation. This histone mark could be modulated by isoniazid (INH), aa preferred and widely used drug for the treatment of latent tuberculosis (TB), via generation of isonicotyl CoA. By RNA-seq analysis, we demonstrate that histone lysine isonicotinylation marks are involved in regulation of gene expression and associated with diverse biological processes. Thereby,enhanced isonicotinylation may represent a mechanism underlying side effects in patients who taking long-term isoniazid and may also increase risk for cancers.

overall_design: We have a control group and a INH-treated group for RNA-seq, each group contains 3 bilogical replicates.

first: Yuhan

last: Jiang


title: m6Am RNA methylation enzyme PCIF1 restricts HIV infection and is degraded by viral Vpr protein

summary: To identify m6Am genes that are responsible for HIV inhibition, MeRIP-seq was performed in control and PCIF1 KO T cells infected with HIV.

overall_design: Control or PCIF1 KO Jurkat cells were mock treated or infected with HIV LAI strain at an MOI of 4 for 3 days. Change of RNA methylation states was detected by MeRIP-seq. m6Am genes were identified as 5'UTR methylated peaks that are depleted in PCIF1 cells


title: The role of H3K36 methylation and associated methyl transferases in chromosome-specific gene regulation

status: Public on Aug 10 2021

city: Umeå

first: Henrik

last: Lindehell

address: Umeå universitet

department: Department of Molecular Biology

country: Sweden

institute: Umeå University

summary: In Drosophila, two chromosomes require special mechanisms to balance their transcriptional output to the rest of the genome. These are the male-specific lethal complex targeting the male X chromosome and Painting of fourth targeting chromosome 4. Here, we explore the role of histone H3 methylated at lysine-36 (H3K36) and the associated methyltransferases—Set2, NSD, and Ash1—in these two chromosome-specific systems. We show that the loss of Set2 impairs the MSL complex–mediated dosage compensation; however, the effect is not recapitulated by H3K36 replacement and indicates an alternative target of Set2. Unexpectedly, balanced transcriptional output from the fourth chromosome requires intact H3K36 and depends on the additive functions of NSD and Ash1. We conclude that H3K36 methylation and the associated methyltransferases are important factors to balance transcriptional output of the male X chromosome and the fourth chromosome. Furthermore, our study highlights the pleiotropic effects of these enzymes.

overall_design: RNA-seq in male third instar larvae brains. 5 brains per sample and between 4 and 7 replicates per condition (Oregon R, Set21 , ash122/ash19011, NSDds46, ash122 NSDds46/ash19011 NSD ds46, ΔHisC; 12xH3K36R, ΔHisC; 12xH3K36K and ΔH3.3B; ΔH3.3A). The sequencing was performed in two rounds and Oregon R was used as wild type control in both sequencing runs.

first: Alexander

last: Glotov

first: Eshagh

last: Dorafshan

first: Yuri

middle: B

last: Schwartz

first: Jan

last: Larsson


title: Mitochondrial BCRP sustains the proliferation and survival of drug-resistant breast-cancer cells by regulating intracellular ROS

status: Public on Aug 08 2021

city: Tianjin

first: He

last: Zhang

state: Tianjin

address: Tianjin 300060

department: Public Laboratory

institute: Tianjin Medical University Cancer Institute and Hospital

summary: ATP-binding cassette (ABC) transporter family are major contributors to the drug-resistance establishment of breast cancer cells. Breast cancer resistant protein (BCRP), one of the ABC transporters, has long been recognized as a pump that effluxes the therapeutic drugs against the concentration gradient. However, recent studies suggest that the biological function of BCRP is not limited in its drug-pump activity. Herein, the role of BCRP in the proliferation and survival of drug-resistant breast cancer cells was investigated. We found that BCRP is not the major drug pump to efflux epirubicin in the resistant cells that express multiple ABC transporters. Silencing of BCRP significantly impairs cell proliferation and induces apoptosis of the resistant cells in vitro and in vivo. RNA-sequencing and high-throughput proteomics suggest that BCRP is an inhibitory factor of oxidative phosphorylation (OXPHOS). Further research suggests that BCRP is localized in the mitochondria of the resistant cells. Knockdown of BCRP elevated the intracellular reactive oxygen species (ROS) level and eventually promotes the cell to undergo apoptosis. This study demonstrated that BCRP exerts important onco-promoting functions in the drug-resistant breast cancer cells independent of its well-recognized drug-efflux activity, which shed new light on understanding the complex functional role of ABC transporters in drug-resistant cells.

overall_design: For transcriptome RNA sequencing (RNA-Seq), SK/EPI, SK-BR-3, SK/EPI-siBCRP and SK/EPI-siNC cells were prepared in triplicates and lysed by Trizol reagent (Invitrogen). Then the cell lysates were processed and sequence by NovoGene (Beijing, China).

first: Xingxing

last: Han

first: Zhaosong

last: Wang

first: Zhiyong

first: Yanfen

last: Cui

first: Ran

last: Tian

first: Yuying

first: Baoai

first: Hui

last: Liu

first: Xiaoyan

last: Zuo

first: Sixin

last: Ren

first: Jianfei

first: Ruifang

last: Niu

first: Fei


title: Real-time quantitative PCR analysis of mouse brainstem oligodendrocytes

city: San Antonio

first: Elizabeth

last: Gould

state: Texas

address: 7703 Floyd Curl Dr

institute: University of Texas Health Science Center San Antonio

summary: Oligodendrocytes were aspirated after electrophysiology recordings for qPCR analysis from cerebellum slices

overall_design: qPCR gene expression profiling.

first: Jun

last: Kim


title: RAC1 is an essential cofactor for estrogen receptor alpha [RNA-seq 2]

last: Sun

overall_design: MCF-7 cells were estrogen-deprived for 3 days before the cells were treated for 1 h during which the newly synthesized RNAs were labeled with BrU. The newly synthesized RNAs were purified and were subjected to RNA-seq.

first: Stephen

last: Nimer

first: Marc

last: Lippman


title: RAC1 is an essential cofactor for estrogen receptor alpha [RNA-seq 1]

overall_design: RNA-seq was performed on MCF-7 cells transfected with siRNA oligo targeting RAC1 after 3 days. MCF-7 cells transfected with non-targeting siRNA oligo served as control.


title: Loss of PRC1 in Uveal melanoma

city: New Haven

first: Mathieu

last: Bakhoum

address: 300 George St.

department: Ophthalmology

institute: Yale University

summary: We demonstrated that loss of Histone 2A Ubiquitination and PRC1 activity drives uveal melanoma progression

overall_design: RNA-seq and CUT&RUN of Uveal melanoma cell lines

first: Jasmine

middle: H

last: Francis

first: Albert

last: Agustinus

first: Ethan

last: Earlie

first: Melody

last: Di Bona

first: David

last: Abramson

first: Mercedes

last: Duran

first: Ignas

last: Masilionis

first: Elsa

last: Molina

first: Alexander

middle: N

last: Shoushtari

first: Michael

last: Goldbaum

first: Paul

last: Mischel

first: Samuel

first: Ashley

last: Laughney


title: A Chemical Probe Based on the PreQ1 Metabolite Enables Transcriptome-wide Mapping of Binding Sites

city: Frederick

first: Curran

last: Rhodes

state: MD

address: 1050 Boyles St.

department: NCI

institute: NIH

summary: We report the optimization and application of diazirine photocrosslinking probes that enable selective covalent crosslinking to the PreQ1 RNA aptamer and any other interacting RNAs in close proximity.  By evaluating the impact of the linker structure and length on crosslinking efficiency we were able to shed important light on what factors have the largest impact on photocrosslinking efficiency in this model system.  Additionally, the best compound (compound 11) was shown to efficiently and selectively crosslink site-specifically to the PreQ1 aptamer even in the presence of competing human cellular RNAs.  Sequencing experiments were performed in human MCF-7 cell total RNA both with and without spike in of exogenous PreQ1 aptamer.  In the aptamer spike-in samples, the only RNA target that was significantly enriched after differential expression analysis with the negative control (compound 17) was the PreQ1 aptamer suggesting that this compound does in fact selectively crosslink to the desired target even in the presence of other RNAs.  Additionally, in the samples without spike-in of the aptamer we were able to identify 16 significantly enriched hit RNAs that may represent novel metabolite-RNA interactions.  Competitive RT-qPCR experiments confirmed enrichment of a handful of select genes with 11 and showed that the free PreQ1 ligand, which lacks the diazrine crosslinking moeity, is able to compete away compound 11.  This suggests that these interactions are specific.

overall_design: Comparison of which RNAs are selectively crosslinked by 11 and 17 under various conditions through sequencing.

first: Sumirtha

last: Balaratnam

first: Desta

last: Bume

first: Colleen

last: Connelly

first: Christopher

last: Lai

first: James

last: Kelley

first: Kamyar

last: Yazdani

first: Phil

last: Homan

first: Danny

last: Incarnato

first: Tomoyuki

last: Numata

first: John

last: Schneekloth Jr


title: Selective loss of resident macrophage derived insulin-like growth factor-1 abolishes adaptive cardiac growth to stress

status: Public on Aug 06 2021

city: Toronto

first: Slava

last: Epelman

state: Ontario

address: 101 College St.

country: Canada

institute: University Health Network

summary: Hypertension affects one-third of the world's population, leading to cardiac dysfunction that is modulated by resident and recruited immune cells. Cardiomyocyte growth is essential to withstand hypertensive stress, however whether immune cells are involved in this cardioprotective process is unclear. In normotensive animals, single-cell transcriptomics of fate-mapped self-renewing cardiac resident macrophages (RMs) revealed transcriptionally diverse cell states with a core repertoire of reparative gene programs, including high expression of Insulin-like Growth Factor-1 (Igf1). Hypertension drove selective in situ proliferation and transcriptional activation of some cardiac RM subsets, directly correlating with increased cardiomyocyte size and cardiac mass. Inducible ablation of RMs, or selective deletion of RM-derived Igf1 caused complete absence of adaptive cardiomyocyte growth and development of cardiac dysfunction without adaptive organ growth. Single cell transcriptomics identified a conserved IGF1-expressing macrophage subpopulation in human cardiomyopathy. Here, we defined the absolute requirement of RM-produced IGF-1 in cardiac adaptation to hypertension.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single cell RNA sequencing of resident cardiac macrophages at steady state and during acute and chronic hypertensive stress in mice.

first: Homaira

last: Hamidzada


title: Mutation of the EPHA2 tyrosine-kinase domain dysregulates cell pattern formation and cytoskeletal gene expression in the lens

status: Public on Aug 05 2021

city: St. Louis

first: Thomas

last: Bennett

address: 660 S Euclid Ave.

summary: Genetic variations in ephrin type-A receptor 2 (EPHA2) have been associated with inherited and age-related forms of cataract in humans. Here we have characterized the eye lens phenotype and transcript profile of germline Epha2 knock-in mutant mice homozygous for either a missense variant associated with age-related cataract in humans (Epha2-Q722) or a novel insertion-deletion mutation (Epha2-indel722) that were both located within the tyrosine-kinase domain of EPHA2. Whole-mount confocal imaging of clear lenses from Epha2-indel722 mice on a fluorescent reporter background revealed misalignment of epithelial-to-fiber cell meridional-rows at the lens equator and severe disturbance of Y-suture formation at the lens poles, whereas, Epha2-Q722 lenses displayed mild disturbance of posterior sutures. Immunofluorescent labeling showed that EPHA2 was mostly localized to lens fiber cell membranes with some sub-membrane localization observed in Epha2-Q722 lenses and diffuse membrane and perinuclear localization in Epha2-indel722 lenses. Immunoprecipitation/blotting studies indicated that EPHA2 formed strong complexes with Src kinase but not with catenin beta 1 or cadherin 2 and was mostly serine phosphorylated in the lens. RNA-sequencing analysis revealed differential expression of several cytoskeleton-associated genes in Epha2-mutant and Epha2-null lenses including strong downregulation of Lgsn and Clic5. Collectively, our data suggest that mutations within the tyrosine-kinase domain of EPHA2 result in lens cell patterning defects and dysregulated expression of several cytoskeletal proteins.

overall_design: mRNA profiles from seven day old lenses of wild type (WT), EPHA2 null, and EPHA2 mutant mice

first: Yuefang

last: Zhou

first: Philip

last: Ruzycki

first: Alan

last: Shiels


title: Short-term MEK inhibitor treatment of genetically engineered mouse model-derived pancreatic cancer cell lines

city: Essen

first: Laura

last: Godfrey

address: Hufelandstraße 55

institute: DKTK Partner Site Essen/Düsseldorf

summary: The impact of short-term MEK inhibition on the gene expression of murine pancretic cancer cell lines was studied.

overall_design: RNA-sequencing of four primary murine pancreatic ductal adenocarcinoma cell lines. Two conditions each (DMSO treated control and 48 h MEKi treatement) were analyzed.

first: Jiangning

last: Gu

first: Jan

last: Forster

first: Sven-Thorsten

last: Liffers

first: Sven

last: Rahmann

first: Jens

middle: T

last: Siveke


title: N6-adenosine Methylation of Enhancer RNAs and YTHDC1 Facilitate Transcriptional Condensate Formation and 3D Chromatin Organization

city: HOUSTON

first: Ruoyu

last: Wang

address: 6431 Fannin St

institute: UTHealth McGovern Medical School

summary: Eukaryotic chromatin is pervasively transcribed into nascent RNAs. However, a mechanistic understanding of their general roles remains lacking. Here, we characterized the landscapes of N6-adenosine methylation (i.e. m6A) on nascent RNAs using a new method that we referred to as MINT-Seq. We found widespread m6A deposition on nascent RNAs produced from regulatory elements including enhancer RNAs (eRNAs) and promoter upstream antisense RNAs (uaRNAs).

overall_design: The lanscape of m6A methylation on enhancer RNAs in human cells using MINT-Seq. We also examined the roles of m6A-eRNAs and YTHDC1 in transcriptional regulation and 3D genome structure with GRO-Seq, TT-Seq, ChIP-Seq and, Hi-C.

first: Wenbo

last: Li

first: Joo-Hyung

last: Lee


title: Effect of Hirudin,Curcumin or Buyang Huanwu Formulas Exposure on  Gene Expression of UUO rats

first: Hangxing

last: Yu

address: No.88 Changling Road, Xiqing District

institute: First Teaching Hospital of Tianjin University of Traditional Chinese Medicine

summary: We performed RNA-Seq analysis to investigate the gene expression patterns in the kidneys of rats with unilateral ureteral obstruction (UUO) treated with hirudin, curcumin or Buyang Huanwu Formula(BHF).

overall_design: The SD rats were randomly divided into a sham group, a unilateral ureteral obstruction (UUO) group, a UUO curcumin-treated group, a UUO hirudin-treated group and a UUO BHF-treated group, with three rats in each group. 40 IU/kg/d was administered intravenously caudally in the hirudin-treated group, while 20 ml/kg/d and 27 ml/kg/d were administered intragastrically in the UUO curcumin-treated and UUO BHF-treated groups, respectively, and sanitary saline (SPSS) was administered intravenously caudally in the UUO and Sham groups. All rats in each group underwent left unilateral ureteral obstruction, except for the Sham group.

first: Kang

last: Yang

first: Wei

last: Lin


title: Microarray analysis of differentially expressed long non-coding RNAs in daidzein-treated lung cancer cells

city: Jiujiang

first: FANG

middle: LAI

last: LI

address: 57 Xunyang East Road

institute: Jiujiang University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Daidzein has been found to significantly inhibit the proliferation of lung cancer cells, while its potential molecular mechanisms remain unclear. To determine the molecular mechanism of daidzein on lung cancer cells, the Capital Bio Technology Human long non-coding (lnc)RNA Array v4, 4x180K chip was used to detect the gene expression profiles of 40,000 lncRNAs and 34,000 mRNAs in a human cancer cell line. Reverse transcription-quantitative (RT-q) PCR analysis was performed to detect the expression levels of target lncRNA and mRNAs in the H1299 cells treated with and without daidzein, using the lncRNA and mRNA gene chip. Bioinformatics analysis was performed to determine the differentially expressed genes from the results of the chip assays. There were 119 and 40 differentially expressed lncRNAs and mRNAs, respectively, that had a 2-fold change in expression level. A total of eight lncRNAs were upregulated in the H1299 lung cancer cells, while 111 lncRNAs were downregulated. Furthermore, five mRNAs were upregulated, and 35 mRNAs were downregulated. A total of six differentially expressed lncRNAs (ENST00000608897.1, ENST00000444196.1, ENST00000608741.1, XR_242163.1, ENST00000505196.1 and ENST00000498032.1) were randomly selected to validate the microarray data, which were consistent with the RT-qPCR analysis results. Differentially expressed mRNAs were enriched in important Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways. Taken together, the results of the present study demonstrated that daidzein affected the expression level of lncRNAs in lung cancer cells, suggesting that daidzein may have potential effects on lung cancer cells.

overall_design: Gene expression of mRNA and lncRNA expression levels between daidzein-treated and-untreated H1299 lung cancer cells, based on the original results of the gene chip.

first: LAIFANG

first: JUN

last: Liu

first: XIAOBO

first: XIAOWEI

last: Xiong

first: SHAOXIN

last: Huang

first: XIN


title: A longitudinal sampling study of transcriptomic and epigenetic profiles in patients with thrombocytopenia syndrome

city: wuhan

first: han

middle: shao

last: qing

address: whu

institute: school

summary: Severe fever with thrombocytopenia syndrome (SFTS) is a new tick-borne infectious disease caused by a new SFTS virus (SFTSV). Due to its 12%-50% high fatality rate and the possibility of pandemic transmission, as well as no specific antiviral drugs for the treatment so far, SFTSV has been listed as one of the top 10 priority infectious diseases by the World Health Organization. Currently, there are rare studies of transcriptomic analysis for the patients infected with SFTSV, which makes it difficult to deeply understand the life cyle and pathogenicity of this virus. To explore the differences of transcripts after SFTSV infection, we performed a longitudinal sampling study to systematically investigate the chronological changes of viral load and transcriptomic and epigenetic characterization using white blood cells from SFTSV patients. The results showed significant changes in the expression of some genes from onset to recovery of SFTSV infection. Moreover, these differentially expressed genes showed good consistency in the three patients at different stages of treatment, which may contribute to the pathophysiology of SFTSV and thus lead to a breakthrough in SFTSV therapy. Moreover, by m6A-seq, we found some genes that might be regulated by m6A. This study in transcript changes and RNA modification may open a brand new direction to our understanding of SFTSV and play an important role in the drugs discovery for effective treatment.

overall_design: RNA-seq and m6A-seq for analysing the differential genes

first: Y

first: S

last: Han

first: R

last: Ran

first: X

last: Weng

last: Zhou


title: Troy/Tnfrsf19 marks epidermal cells that govern interfollicular epidermal renewal and cornification

city: Würzburg

first: Kai

last: Kretzschmar

address: Josef-Schneider-Str. 2

institute: University Hospital Würzburg

summary: The skin epidermis is a highly compartmentalised tissue consisting of a cornifying epithelium called the interfollicular epidermis (IFE) and associated hair follicles (HFs). Several stem cell populations have been described that mark specific sub compartments in the skin but none of them is IFE-specific. Here we identify Troy as a marker of IFE and HF infundibulum basal layer cells in embryonic and adult human and mouse epidermis. Genetic lineage-tracing experiments demonstrate that Troy-expressing basal cells contribute to long-term renewal of all layers of the cornifying epithelium. Single-cell transcriptomics and organoid assays of Troy-expressing cells as well as their progeny confirmed stem cell identity as well as the ability to generate differentiating daughter cells. In conclusion, we define Troy as a marker of epidermal basal cells that govern interfollicular epidermal renewal and cornification.

overall_design: We generated single-cell and bulk transcriptome data from epidermal keratinocytes collected from adult murine skin epidermis.

first: Kim

last: Boonekamp

first: Margit

last: Bleijs

first: Priyanca

last: Asra

first: Mandy

last: Koomen

first: Susana

middle: M

last: Chuva de Sousa Lopes

first: Barbara

last: Giovannone

first: Hans

last: Clevers


title: Confronting false discoveries in single-cell differential expression

status: Public on Aug 04 2021

city: Vancouver

first: Jordan

middle: W

last: Squair

state: BC

address: 818 West 10th Avenue

institute: University of British Columbia

summary: Differential expression analysis in single-cell transcriptomics enables the dissection of cell-type-specific responses to perturbations such as disease, trauma, or experimental manipulations. While many statistical methods are available to identify differentially expressed genes, the principles that distinguish these methods and their performance remain unclear. Here, we show that the relative performance of these methods is contingent on their ability to account for variation between biological replicates. Methods that ignore this inevitable variation are biased and prone to false discoveries. Indeed, the most widely used methods can discover hundreds of differentially expressed genes in the absence of biological differences. To exemplify these principles, we exposed true and false discoveries of differentially expressed genes in the injured mouse spinal cord.

overall_design: We performed experiments in mice that underwent a severe contusion of the thoracic spinal cord and in uninjured controls. After six weeks of recovery, we harvested the lumbar spinal cord below the injury, and performed single-nucleus RNA-seq (snRNA-seq) of these tissues. We sequenced a total of 19,237 cells that encompassed all the major cell types of the lumbar spinal cord.

first: Matthieu

last: Gautier

first: Claudia

last: Kathe

first: Mark

last: Anderson

first: Nicholas

last: James

first: Thomas

last: Hutson

first: Rémi

last: Hudelle

first: Kaya

last: Matson

first: Quentin

last: Barraud

first: Ariel

last: Levine

first: Gioele

last: La Manno

first: Michael

last: Skinnider

first: Grégoire

last: Courtine


title: Gene expression of two Ewing sarcoma cell lines (SK-N-MC, RDES), transfected with inducible shControl or two different shRNA against PRC1

city: Heidelberg

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

institute: German Cancer Research Center (DKFZ)

summary: This dataset comprises trnscriptome data of two Ewing sarcoma cell lines (SK-N-MC and RDES) after knockdown of the gene PRC1

overall_design: 12 samples were normalized (log2) with Affymetrix Expression Console Software (v1.4) using SST-RMA algorithm. Gene expression data were annotated at gene level with the Affymetrix library for Clariom D arrays (human).

first: Jing

last: Li

first: Martin

last: Orth

middle: G

last: Grünewald


title: Transcriptomic response to Keap1-specific electrophile modification in zebrafish embryos

city: Boston

first: Jesse

last: Poganik

address: 77 Avenue Louis Pasteur

department: Medicine/Genetics

institute: Brigham and Women's Hospital, Harvard Medical School

summary: Using our eletrophile delivery platform in zebrafish embryos (termed "Z-REX"), we launched a Z-REX-coupled RNA-seq screen to identify genes whose expression is significantly changed following Keap1-engagement with selective native lipid-derived electrophiles housing covalently-reactive motifs. The electrophiles tested were 4-hydroxynonenal (HNE) and 4-hydroxydodecenal (HDE).

overall_design: Three samples were analyzed with one replicate per condition: non-treated fish, fish subjected to HNE Z-REX, and fish subjected to HDE Z-REX.

first: Marcus

last: Long

first: Saba

last: Parvez

first: Yimon

last: Aye


title: NRF2 signalling associated with radioresistance in colorectal cancer models

status: Public on Aug 03 2021

city: Oxford

first: Sean

middle: Micheal

last: O'Cathail

state: State...

address: Old Road Campus Research Building

department: Oncology

institute: CRUK/MRC Oxford Institute for Radiation Oncology

summary: Whole transcriptome profiles from radiosenstised siNRF2 treated SW1463 and radioresistant HCT116 NRF2 E79K+ mutant colorectal cancer cell lines

overall_design: Radiosenstised siNRF2 treated SW1463 and radioresistant HCT116 NRF2 E79K+ mutant colorectal cancer cell lines


title: Analysis of skin of keratinocyte-specific OTULIN-deficient mice by single-cell RNA-sequencing

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

summary: In order to unravel the functional role of the linear deubiquitinase OTULIN, we performed single-cell RNA-sequencing on total skin of mice lacking OTULIN selectively in keratinocytes. Keratinocyte-specific OTULIN knock-out (KO) mice develop delineated inflammatory lesion. Through single-cell analysis on lesional and non-lesional skin of mice lacking OTULIN in keratinocytes, we could identify signalling pathways through which these inflammatory lesions appear, allowing us to get new insights on the molecular events that regulate skin homeostasis and mediate skin inflammation.

overall_design: The purpose of this study was to delineate the cellular and molecular changes that occur in the skin when linear deubiquitination is absent in keratinocytes. Total skin was harvested from wild-type (WT) skin and lesional and non-lesional keratinocyte-specific OTULIN knock-out (KO) mice. We FACS sorted live cells from single-cell suspensions of total skin.

first: Esther

last: Hoste

first: Kim

last: Lecomte

first: Karl

last: Annusver

first: Niels

last: Vandamme

first: Jana

last: Roels

first: Sophia

last: Maschalidi

first: Lien

last: Verboom

first: Hanna-Kaisa

last: Vikkula

first: Mozes

last: Sze

first: Lisette

last: Van Hove

first: Kevin

last: Verstaen

first: Arne

last: Martens

first: Tino

last: Hochepied

first: Yvan

last: Saeys

first: Kodi

last: Ravichandran

first: Maria

last: Kasper

first: Geert

last: van Loo


title: MicroRNA sequencing of BIBINS HIE dried blood spot

city: London

first: Ping

last: Yip

address: 4 Newark St

department: Blizard Institute

institute: Queen Mary University of London

summary: Able to seqence microRNA from 2 x 6 mm dired blood spot chads from the BIBINS study. Samples are from newborns with moderate-severe HIE undergoing therapeutic hypothermia at around 16-24 h post insult, mild HIE without therapeutic hypothermia, and umbilical cord blodd from normal pregnancies.

overall_design: Examine first blood samples collected in the form of dried blood spots

middle: K

first: Divyen

last: Shah

first: Vennila

last: Ponnusamy


title: IgG4-ROD and orbital MALT lymphoma

status: Public on Aug 01 2021

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: The molecular pathogenesis of orbital lymphoproliferative disorders, such as immunoglobulin G4-related ophthalmic disease (IgG4-ROD) and orbital mucosa-associated lymphoid tissue (MALT) lymphoma, remains essentially unknown. Differentiation between the two disorders, which is important since work-up and treatment can vary greatly, is often challenging due to the lack of specific biomarkers. Although miRNAs play an important role in the regulation of carcinogenesis and inflammation, the relationship between miRNA and orbital lymphoproliferative diseases remains unknown. A comprehensive analysis of 2,565 miRNAs was performed in biopsied specimens and serum of 17 cases with IgG4-ROD and 21 cases with orbital MALT lymphoma. We identified specific miRNA signatures, their miRNA target pathways, and network analysis associated with IgG4-ROD and orbital MALT lymphoma. Machine-learning analysis identified miR-202-3p and miR-7112-3p as the best discriminators of IgG4-ROD and orbital MALT lymphoma, respectively. In the tissue pathway, Longevity regulating pathway in IgG4-ROD and MAPK signaling pathway in orbital MALT lymphoma were most enriched by downregulated miRNAs. This is the first evidence of the miRNA profile in biopsied specimens and serum of patients with IgG4-ROD and orbital MALT lymphoma. These data will be useful for developing diagnostic and therapeutic interventions, as well as elucidating of these disorders.

overall_design: A total of 14 biopsied specimen of patients with 6 IgG4 related ophthalmic disease (IgG4-ROD) and 8 orbital mucosa associated lymphoid tissue (MALT) lymphoma and a total of 35 serum of patients with 11 IgG4-ROD, 13 orbital MALT lymphoma and 11 healthy individual were characterized using the 3D-Gene® Human miRNA Oligo Chip (Toray Industries, Inc.).

first: Naoya

last: Nezu

first: Yoshihiko

last: Usui


title: DNA methylome regulation by progesterone receptor in primary leiomyoma cells

city: Chicago

first: Shimeng

last: Liu

state: Illinois

address: 320 East Superior Street

institute: Northwestern University

summary: Uterine leiomyomas (LM) affect up to 80% of all reproductive-age women. LM growth requires progesterone, progesterone receptor (PGR), and the maintenance and proliferation of a small (5%) stem cell population. Stem cell activation and differentiation are driven by DNA methylation and nuclear hormone receptor action, but crosstalk between these mechanisms remains unclear. We performed an integrated analysis of the transcriptome and epigenetic landscape of LM cells at three differentiation stages and the PGR cistrome of whole LM tissue. The PGR-deficient stem cell population harbored a unique methylation landscape, with hypermethylation at the PGR gene locus and PGR-binding regions, which suppressed stem cell responsiveness to progesterone. The DNA methylation inhibitor 5’-Aza upregulated the expression of PGR and its target genes by stimulating PGR recruitment to the targeted gene loci, and significantly depleted the LM stem cell population and its tumor-initiating capacity.  We herein provided mechanistic insights via therapeutically accelerating the stem cell differentiation process of a hormone-sensitive tumor.

overall_design: Identify DNA methylome changes between siCtrl and siPGR in  primary LM cells using RNA-Seq

last: Yin

first: Serdar

last: Bulun


title: SPOP mutations derived from prostate cancer establish a DNA hypermethylation epigenome through stabilizing GLP histone methyltransferase

city: Rochester

first: Ting

last: Wei

state: MN

address: 507 3rd St SW

institute: Mayo Clinic

summary: Abnormal DNA methylation is one of the major factors driving oncogenesis and therapy resistance in cancer. The CULLIN3-RBX1 E3 ubiquitin ligase adaptor gene SPOP is the most frequently mutated gene in primary prostate cancers (PCa). SPOP-mutated prostate tumors strikingly associate with strongly elevated levels of genome-wide DNA hypermethylation, although the underlying mechanism remains elusive. We use reduced representation bisulfite sequencing (RRBS) to depict DNA methylation in control and SPOP F133V stably expressed 22Rv1 cells. Genomic DNA of cells are extracted and treated with restriction enzyme and followed by bisulfite sequencing to enrich for areas of the genome with a high CpG content. We find that SPOP mutant expression increases not only the overall cellular level of DNA methylation, but also specifically at loci of a subset of tumor suppressor genes (TSG) including FOXO3 and NDRG1, and this effect is mediated by GLP/G9a binding with DNMT proteins. These findings reveal a previously uncharacterized mechanism by which SPOP mutations promote DNA hypermethylation through stabilization GLP as a chromatin recruiter of DNMT. Our results also suggest that targeting DNA hypermethylation is a viable strategy for effective management of SPOP mutated PCa.

overall_design: Examination of DNA methylation in SPOP WT and SPOP F133V Pca cell line.

first: Haojie

last: Huang

first: Jianong

last: Zhang

first: Liguo

last: Wang

first: Zhenqing

last: Ye